I have seen a bunch of double elimination tournaments in different games.
You are right that the logical structure of the grand finals (in the double elim spirit) is 2 sets of BO3 and the team from lower bracket needs to win both sets individually.
That being said, there are other factors when deciding the format. Most importantly what's attractive for the viewers. 2 sets of finals series can be confusing to casual viewers and it's also potentially quite long.
Most events in many sports and games choose not to do it.
Some events give some other kind of advantage to the team advancing from winners bracket (such as a 1:0 lead in a BO5 or BO7, option to pick the first map, choose side or some other "coin toss win" for the first game depending on what game it is).
Many others choose to not give an explicit advantage and the fact that team in a losers bracket had to go through more series is considered a disadvantage enough (for example, in the MDI, Method NA only won 3 series while KJA won 5; one could argue that 5:1 is better than 3:1).
At the end of the day, I think it's fair to lobby for a format you consider better, but that's something to do before the event.
Once the format is known to all participants, everyone knows what to expect and it's by no means unfair.
In the case of WoW dungeons, 2 sets of series would be fine with me, winner bracket team having first pick of the map would be ok as well I guess.
Having a 1:0 advantage is way too much though. It's fine in other games (such as MOBAs), where the individual rounds are balanced and you have equal chance of winning each game. In WoW that's not the case because different dungeons favor different comps (and therefore teams).
Also, if you want to point out potentially slightly unfair format decisions, how is it fair that Europe only gets 2 spots (same as China/Americas/Australia) given the results of time trials?